In order to protect Jakarta from the flood hazard due to sea level rise and land subsidence, Government of Indonesia initiates a masterplan to resolve this. The masterplan is called National Capital Integrated Coastal Development (NCICD). One of its action plans is to build a Giant Sea Wall along the Jakarta Bay. In this research, the possible effects of NCICD to the urban drainage system will be discussed. For that purpose, it is proposed that Jakarta can be divided into 5 compartments; each compartment has area of approximately 10,000 ha and delineated based on existing main drainage systems (natural drainage) and other physical boundaries e.g. roads which border one compartment to another. In this case, one compartment will be evaluated on their hydraulic performance. It is so called Compartment 2. Located in northern of Jakarta and at the northern boundary, this compartment is bordered by the inner dikes of the coming NCICD project. From the model simulation, it can be concluded that in general pumping capacity in combination with the open storage areas are sufficient and all the pumps should be operated simultaneously. Compartment system could be useful in order to mitigate the flood in Jakarta area. By considering practical aspects of the water management system, the service area of a compartment should not be too large or too small. The model shows that the effect of the land reclamation NCICD to the water levels along the main drainage system (Ciliwung River). The water level (_h) will increase between 0.8 m at the downstream to 0.2 m at the upstream. To avoid overtopping, the crest elevation of the river embankments has to be increased. It is suggested that in Phase A of NCICD should also strengthen and improve the dikes along the main drainage system, and not only the existing dikes along the coastlines. A proper operation of water management is really required in Giant Sea Wall as an integrated system when Phase A and Phase B are completed. This wall is planned to be constructed in a fully controlled system, creating a giant artificial lake. In case the land subsidence will continue, it means that water level in the lake will be lower and lower in time. If the water level in the lake decreases, it will also affect the water level along the rivers which flow into the lake (dry season). Hence, a proper water management has to be established.